Fetch data from remote databases. — db • valr

Currently db_ucsc and db_ensembl are available for connections.

Usage

db_ucsc(
  dbname,
  host = "genome-mysql.cse.ucsc.edu",
  user = "genomep",
  password = "password",
  port = 3306,
  ...
)

db_ensembl(
  dbname,
  host = "ensembldb.ensembl.org",
  user = "anonymous",
  password = "",
  port = 3306,
  ...
)

Arguments

dbname: name of database
host: hostname
user: username
password: password
port: MySQL connection port
...: params for connection

See also

https://genome.ucsc.edu/goldenpath/help/mysql.html

https://www.ensembl.org/info/data/mysql.html

Examples

if (FALSE) {
if (require(RMariaDB)) {
  library(dplyr)
  ucsc <- db_ucsc("hg38")

  # fetch the `refGene` tbl
  tbl(ucsc, "refGene")

  # the `chromInfo` tbls have size information
  tbl(ucsc, "chromInfo")
}
}
if (FALSE) {
if (require(RMariaDB)) {
  library(dplyr)
  # squirrel genome
  ensembl <- db_ensembl("spermophilus_tridecemlineatus_core_67_2")

  tbl(ensembl, "gene")
}
}